CHANGELOG.md

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

[v0.2.5]

Added

• Added batch_size parameter to Kernel.compute_neighbors() for backend-agnostic batching {pr}60
• Added subset parameter to plot_confusion_matrix() for filtering cells {pr}60
• Added Python 3.14 support {pr}62

Changed

• Default postfixes now include underscore: "_pred" and "_conf" instead of "pred" and "conf" {pr}60
• Switched from MathJax to KaTeX for documentation math rendering {pr}61
• Updated GitHub Actions to latest versions (checkout v5, setup-uv v7) {pr}61
• Updated test matrix to Python 3.11/3.14 {pr}62

Fixed

• Fixed PackageNotFoundError when checking rapids availability in conda environments {pr}60
• Fixed stale k-NN state when compute_neighbors() fails {pr}60
• Fixed plot_confusion_matrix() handling of NaN values in both y_true and y_pred {pr}60
• Fixed plot_confusion_matrix() handling of mismatched category sets {pr}60
• Fixed plot_confusion_matrix() handling of float categories {pr}60
• Fixed importlib.resources.files() compatibility with Python 3.14 {pr}62

[v0.2.4]

Changed

• Deprecated Python 3.10 support {pr}55
• Updated to cookiecutter-scverse template v0.6.0 {pr}54

[v0.2.3]

Changed

• Improved returning probabilities (after mapping categorical obs fields) to always return a DataFrame {pr}49

Added

• Add the possibility to adjust the library size after .map_layers {pr}50
• Added the option to turn off post-processing of the presence scores, so that they can be first smoothed and then processed, like in HNOCA-tools {pr}51

[v0.2.2]

Added

• Enabled subsetting categories before mapping .obs values {pr}46

Changed

• Updated the README a bit {pr}44
• Updated tutorials to work with new parameter names {pr}43

Fixed

• Fixed a small bug where hvg masks would not be propagated correctly to joint pca computation {pr}48

[v0.2.1]

Changed

• Move some duplicated docstrings into a central _docs.py file {pr}41

Added

• Added some tests for edge cases in the MappingOperator class {pr}41
• Treat faiss-cpu and faiss-gpu separately {pr}41

[v0.2.0]

Added

• Added a tutorial on same-modality query to reference mapping {pr}38
• Added a tutorial on data smoothing {pr}37
• Added an option to return the mapping probabilities for categorical .obs mapping {pr}39
• Added a MappingOperator class which allows for iterative mapping matrix applicatino in self-mapping mode {pr}35
• Add the umap method to compute symmetric k-NN connectivities in self-mapping mode {pr}34

Changed

• Refectored the neighbors classes into a Neighobrs and a Kernel class and moved symmetrization into the Kernel class {pr}36

[v0.1.4]

Changed

• Rename mapping methods to map_obs, map_obsm, and map_layers, and improve support for numerical .obs annotations {pr}30.

[v0.1.3]

Added

• Added a tutorial on spatial contextualization and niche identification {pr}23.
• Implemented a self-mapping mode with only a query dataset {pr}21.
• Allow importing a pre-computed dataset of transfered expression values {pr}21.
• Allow importing pre-computed neighborhood matrices {pr}21.
• Add a tutorial on spatial contextualization and niche identification {pr}21.
• Add an equal-weight kernel {pr}22.

[v0.1.2]

Added

• Included tests for the check module, and more tests for the main classes {pr}15.
• Implemented the computation of presence scores, following HNOCA-tools {pr}16.
• Added a groupby parameter to expression transfer evaluation {pr}16.
• Added a test_var_key parameter to expression transfer evaluation {pr}19.
• Added a tutorial on spatial mapping {pr}19.

[v0.1.1]

Changed

• Switched to vcs-based versioning {pr}5.

Added

• Added PyPI badge.

[v0.1.0]

Initial package release.